Tricky task with DNA sequences. Post: 302551791

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lastal

LASTAL(1)							   User Commands							 LASTAL(1)

NAME

       lastal - genome-scale comparison of biological sequences

SYNOPSIS

       lastal [options] lastdb-name fasta-sequence-file(s)

DESCRIPTION

       Find local sequence alignments.

       Score  options  (default  settings): -r: match score   (DNA: 1, protein: blosum62, 0<Q<5:  6) -q: mismatch cost (DNA: 1, protein: blosum62,
       0<Q<5: 18) -p: file for residue pair scores -a: gap existence cost (DNA: 7, protein: 11, 0<Q<5: 21) -b: gap extension cost  (DNA:  1,  pro-
       tein:   2,  0<Q<5:   9)	-c:  unaligned	residue  pair cost (100000) -F: frameshift cost (off) -x: maximum score drop for gapped alignments
       (max[y, a+b*20]) -y: maximum score drop for gapless alignments (t*10) -z: maximum score drop for final gapped alignments  (x)  -d:  minimum
       score for gapless alignments (e*3/5) -e: minimum score for gapped alignments (DNA: 40, protein: 100, 0<Q<5: 180)

       Cosmetic  options  (default  settings): -h: show all options and their default settings -v: be verbose: write messages about what lastal is
       doing -o: output file -f: output format: 0=tabular, 1=maf (1)

       Miscellaneous options (default settings): -s: strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein) -m: maximum multiplicity  for
       initial	matches (10) -l: minimum length for initial matches (1) -n: maximum number of gapless alignments per query position (infinity) -k:
       step-size along the query sequence (1) -i: query batch size (1 MiB if Q>0, else 16 MiB if j=0, else 128	MiB)  -u:  mask  lowercase  during
       extensions: 0=never, 1=gapless,

	      2=gapless+gapped but not final, 3=always (2 if lastdb -c and Q<5, else 0)

       -w:  supress  repeats  inside exact matches, offset by this distance or less (1000) -G: genetic code file -t: 'temperature' for calculating
       probabilities (1/lambda) -g: 'gamma' parameter for gamma-centroid and LAMA (1) -j: output  type:  0=match  counts,  1=gapless,  2=redundant
       gapped, 3=gapped,

	      4=column ambiguity estimates, 5=gamma-centroid, 6=LAMA (3)

       -Q: input format: 0=fasta, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina,

	      4=prb, 5=PSSM (0)

REPORTING BUGS

       Report bugs to: last (ATmark) cbrc (dot) jp
       LAST home page: http://last.cbrc.jp/

lastal 199							     May 2012								 LASTAL(1)